#!/bin/bash

treedir=$1
treeprefix=$2
input_reads=$3
max_occurences=$4

if [ $# == 4 ]; then 
	time(./sortReads $input_reads $input_reads.sortReads)
	time(./blindSearch $treedir $treeprefix $input_reads.sortReads $max_occurences)
	time(./validateMatches $treedir $treeprefix $input_reads.sortReads.blindSearch $input_reads $max_occurences)
	
else
	echo "usage: $0 suffix_tree_directory tree_prefix input_fasta maximum_occurences"
fi



